nDNA -- the Semantic Helix of Artificial Cognition

Abstract

As AI foundation models grow in capability, a deeper question emerges: What shapes their internal cognitive identity -- beyond fluency and output? Benchmarks measure behavior, but the soul of a model resides in its latent geometry. In this work, we propose Neural DNA (nDNA) as a semantic-genotypic representation that captures this latent identity through the intrinsic geometry of belief. At its core, nDNA is synthesized from three principled and indispensable dimensions of latent geometry: spectral curvature, which reveals the curvature of conceptual flow across layers; thermodynamic length, which quantifies the semantic effort required to traverse representational transitions through layers; and belief vector field, which delineates the semantic torsion fields that guide a model's belief directional orientations. Like biological DNA, it encodes ancestry, mutation, and semantic inheritance, found in finetuning and alignment scars, cultural imprints, and architectural drift. In naming it, we open a new field: Neural Genomics, where models are not just tools, but digital semantic organisms with traceable inner cognition. Modeling statement. We read AI foundation models as semantic fluid dynamics: meaning is transported through layers like fluid in a shaped conduit; nDNA is the physics-grade readout of that flow -- a geometry-first measure of how meaning is bent, paid for, and pushed -- yielding a stable, coordinate-free neural DNA fingerprint tied to on-input behavior; with this fingerprint we cross into biology: tracing lineages across pretraining, fine-tuning, alignment, pruning, distillation, and merges; measuring inheritance between checkpoints; detecting drift as traits shift under new data or objectives; and, ultimately, studying the evolution of artificial cognition to compare models, diagnose risks, and govern change over time.